Job ID = 10223779 SRX = ERX4439558 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:00:56 prefetch.2.10.7: 1) Downloading 'ERR4501487'... 2020-10-15T23:00:57 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:01:33 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:01:33 prefetch.2.10.7: 'ERR4501487' is valid 2020-10-15T23:01:33 prefetch.2.10.7: 1) 'ERR4501487' was downloaded successfully 2020-10-15T23:02:01 prefetch.2.10.7: 'ERR4501487' has 5 unresolved dependencies 2020-10-15T23:02:01 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:02:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:12 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:12 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:02:12 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:02:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:25 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:25 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:02:25 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:02:25 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:37 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:37 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:02:37 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:02:37 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:50 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:50 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:02:50 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:02:50 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:59 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:59 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3564484 spots for ERR4501487/ERR4501487.sra Written 3564484 spots for ERR4501487/ERR4501487.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:44 3564484 reads; of these: 3564484 (100.00%) were paired; of these: 744074 (20.87%) aligned concordantly 0 times 2253101 (63.21%) aligned concordantly exactly 1 time 567309 (15.92%) aligned concordantly >1 times ---- 744074 pairs aligned concordantly 0 times; of these: 317884 (42.72%) aligned discordantly 1 time ---- 426190 pairs aligned 0 times concordantly or discordantly; of these: 852380 mates make up the pairs; of these: 611158 (71.70%) aligned 0 times 53086 (6.23%) aligned exactly 1 time 188136 (22.07%) aligned >1 times 91.43% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 137583 / 3111058 = 0.0442 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:09:34: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:09:34: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:09:40: 1000000 INFO @ Fri, 16 Oct 2020 08:09:45: 2000000 INFO @ Fri, 16 Oct 2020 08:09:51: 3000000 INFO @ Fri, 16 Oct 2020 08:09:57: 4000000 INFO @ Fri, 16 Oct 2020 08:10:02: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:10:04: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:10:04: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:10:08: 6000000 INFO @ Fri, 16 Oct 2020 08:10:09: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:10:09: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:10:09: #1 total tags in treatment: 2700386 INFO @ Fri, 16 Oct 2020 08:10:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:10:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:10:09: #1 tags after filtering in treatment: 2027925 INFO @ Fri, 16 Oct 2020 08:10:09: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 16 Oct 2020 08:10:09: #1 finished! INFO @ Fri, 16 Oct 2020 08:10:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:10:09: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 08:10:09: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 08:10:09: start model_add_line... INFO @ Fri, 16 Oct 2020 08:10:09: start X-correlation... INFO @ Fri, 16 Oct 2020 08:10:09: end of X-cor INFO @ Fri, 16 Oct 2020 08:10:09: #2 finished! INFO @ Fri, 16 Oct 2020 08:10:09: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Oct 2020 08:10:09: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Oct 2020 08:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05_model.r WARNING @ Fri, 16 Oct 2020 08:10:09: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:10:09: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 16 Oct 2020 08:10:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:10:09: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:10:10: 1000000 INFO @ Fri, 16 Oct 2020 08:10:15: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:10:16: 2000000 INFO @ Fri, 16 Oct 2020 08:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.05_summits.bed INFO @ Fri, 16 Oct 2020 08:10:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1306 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:10:21: 3000000 INFO @ Fri, 16 Oct 2020 08:10:27: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:10:32: 5000000 INFO @ Fri, 16 Oct 2020 08:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:10:34: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:10:34: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:10:38: 6000000 INFO @ Fri, 16 Oct 2020 08:10:40: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:10:40: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:10:40: #1 total tags in treatment: 2700386 INFO @ Fri, 16 Oct 2020 08:10:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:10:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:10:40: #1 tags after filtering in treatment: 2027925 INFO @ Fri, 16 Oct 2020 08:10:40: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 16 Oct 2020 08:10:40: #1 finished! INFO @ Fri, 16 Oct 2020 08:10:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:10:40: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 08:10:40: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 08:10:40: start model_add_line... INFO @ Fri, 16 Oct 2020 08:10:40: start X-correlation... INFO @ Fri, 16 Oct 2020 08:10:40: end of X-cor INFO @ Fri, 16 Oct 2020 08:10:40: #2 finished! INFO @ Fri, 16 Oct 2020 08:10:40: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Oct 2020 08:10:40: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Oct 2020 08:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10_model.r WARNING @ Fri, 16 Oct 2020 08:10:40: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:10:40: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 16 Oct 2020 08:10:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:10:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:10:41: 1000000 INFO @ Fri, 16 Oct 2020 08:10:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.10_summits.bed INFO @ Fri, 16 Oct 2020 08:10:47: 2000000 INFO @ Fri, 16 Oct 2020 08:10:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:10:53: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:11:00: 4000000 INFO @ Fri, 16 Oct 2020 08:11:06: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:11:13: 6000000 INFO @ Fri, 16 Oct 2020 08:11:15: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:11:15: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:11:15: #1 total tags in treatment: 2700386 INFO @ Fri, 16 Oct 2020 08:11:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:11:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:11:15: #1 tags after filtering in treatment: 2027925 INFO @ Fri, 16 Oct 2020 08:11:15: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 16 Oct 2020 08:11:15: #1 finished! INFO @ Fri, 16 Oct 2020 08:11:15: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:11:15: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 08:11:15: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 08:11:15: start model_add_line... INFO @ Fri, 16 Oct 2020 08:11:15: start X-correlation... INFO @ Fri, 16 Oct 2020 08:11:15: end of X-cor INFO @ Fri, 16 Oct 2020 08:11:15: #2 finished! INFO @ Fri, 16 Oct 2020 08:11:15: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Oct 2020 08:11:15: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Oct 2020 08:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20_model.r WARNING @ Fri, 16 Oct 2020 08:11:15: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:11:15: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 16 Oct 2020 08:11:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:11:15: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:11:20: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:11:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:11:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439558/ERX4439558.20_summits.bed INFO @ Fri, 16 Oct 2020 08:11:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 2 millis CompletedMACS2peakCalling